淡水豚类线粒体DNA 12S rRNA基因的序列变异及其分子系统学研究

淡水豚类４个代表属「白暨豚（Ｌｉｐｏｔｅｓ）、恒河豚（Ｐｌａｔａｎｉｓｔａ）、弗西豚（Ｐｏｎｔｏｐｏｒｉａ）和亚河豚（Ｉｎｉａ）」ｍｔＤＮＡ １２Ｓ ｒＲＮＡ基因的序列差异水平,高于其他齿鲸类科间的差异,特别是远远高于海豚总科内的科间差异。研究结果支持它们应归属于不同的科,即白暨豚科（Ｌｉｐｏｔｉｉｄａｅ）、恒河豚科（Ｐｌａｔａｎｉｓｔｉｄａｅ）、弗西豚科（Ｐｏｎｔｏｐｏｒｉｄａｅ）和亚河豚科（Ｉ     

Phylogeny of Thalassinidea (Crustacea, Decapoda) inferred from three rDNA sequences: implications for morphological evolution and superfamily classification

The infraorder Thalassinidea is a group of cryptic marine burrowing decapods of which the higher taxonomy is often contentious. The present analysis attempts to reconstruct phylogenetic relationship among 12 of the 13 currently recognized families using partial nuclear 18S, 28S rDNA and mitochondrial 16S rDNA sequences. The infraorder is divided into two distinct clades, with the first clade consisting of Thalassinidae, Laomediidae, Axianassidae and Upogebiidae, and the second clade including Axiidae, Calocarididae, Eiconaxiidae, Callianassidae, Ctenochelidae, Micheleidae, Strahlaxiidae and Callianideidae. Within the first clade, the Upogebiidae is the basal family. The Axianassidae shows low affinity to other laomediid genera indicating that it is a valid family. The interfamilial relationships are less well resolved in the second clade. The Axiidae is paraphyletic with respect to Calocarididae and Eiconaxiidae. Thus, the status of these two latter families is not supported if the currently defined Axiidae is maintained. All three families appear to be basal in the thalassinidean clade. The Micheleidae is closely related to the Callianideidae and they form a sister group to the Strahlaxiidae. The monophyletic Callianassidae aligns with the Micheleidae + Callianideidae + Strahlaxiidae clade. The relationship among the Axiidae + Calocarididae + Eiconaxiidae clade, Callianassidae + Micheleidae + Callianideidae + Strahlaxiidae clade and the Ctenochelidae cannot be resolved which might be due to a rapid radiation of the three lineages. Our results do not support the generally used classification scheme of Thalassinidea and suggest that the infraorder might be divided into two superfamilies instead of three as suggested based on larval morphology, second pereiopod morphology in adults and gastric mill structure. The two superfamilies are Thalassinoidea (i.e. Thalassinidae, Laomediidae, Upogebiidae and Axianassidae) and Callianassoidea (i.e. Axioidea + Callianassoidea, as defined in Martin and Davis (2001) but excluding Laomediidae and Upogebiidae). It also appears that gill‐cleaning adaptations are important in thalassinidean evolution while the presence of linea thalassinica is a result of parallel evolution.     

Bacterial population in Russian space station "Mir"

We had the opportunity to investigate the bacterial population in air samples, condensation water, and inner wall swabs from the Russian space station Mir. From the first and second air samples during the mission, 29 and 7 bacterial colonies were collected, respectively. The values were equivalent to 16.8 and 4.0 cfu/100 liter air, respectively. Condensation water was collected from three different sites. The total viable bacterial counts were 2.1 x 10(6), 5.2 x 10(2), and 3.0 x 10(1) cfu/ml. The phylogenetic position of each isolate was determined by total 16S rDNA sequencing. Bacteria from air samples were mainly Gram-positive (35/36 colonies), and staphylococci occupied dominant specifically (23/36 colonies). On the other hand, Gram-negative bacteria were mainly isolated from condensation water samples. Most strains were thought to be opportunistic pathogens or environmental bacteria (such as those that inhabit soil, water, or air) found on earth. However, 6 of 23 isolates were suspected to be new species according to phylogenetic analysis and quantitative DNA-DNA hybridization data. The isolation of the other levels 3 and 2 bacteria, using specific selective media, was unsuccessful because all samples were heavily contaminated with fungi. To overcome this situation, PCR methods were applied to survey most levels 3 and 2 pathogenic bacteria in the condensation water samples. Up to 380 different primers for bacterial pathogens were used in this study. Only Mycobacterium avium 16S DNA sequences, however, could be amplified from the three water samples. The average bacteria count was estimated to be about 10(4) organisms/ml water.     

从12S rRNA基因第三结构域序列分析探讨蜘蛛若干重要类群的亲缘关系

本文将12S rRNA基因序列分析应用于研究若干重要蜘蛛类群的系统关系,以对传统的分类研究结论进行验证和补充,并且探讨12S rRNA基因序列分析在蜘蛛系统发生研究中的适用性。根据12S rRNA基因第3结构域构建的分子系统树得出结论:1.圆网类(即妖面蛛总科与园蛛总科)并非单系;2.隙蛛与暗蛛较漏斗蛛具有更近的亲缘关系;3.壁钱和拟壁钱并不近缘;4.有筛器类蜘蛛为复系类群;5.12S rRNA基因第3结构域片段对推断近缘科属间的系统发生关系是有效的遗传标记。     

Coexistence of mitochondrial 12S rRNA C1494T and CO1/tRNA(Ser(UCN)) G7444A mutations in two Han Chinese pedigrees with aminoglycoside-induced and non-syndromic hearing loss

Mutations in mitochondrial DNA are one of the important causes of hearing loss. We report here the clinical, genetic, and molecular characterization of two Han Chinese pedigrees with maternally transmitted aminoglycoside-induced and nonsyndromic bilateral hearing loss. Clinical evaluation revealed the wide range of severity, age-at-onset, and audiometric configuration of hearing impairment in matrilineal relatives in these families. The penetrances of hearing loss in these pedigrees were 20% and 18%, when aminoglycoside-induced deafness was included. When the effect of aminoglycosides was excluded, the penetrances of hearing loss in these seven pedigrees were 10% and 15%. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the presence of the deafness-associated 12S rRNA C1494T and CO1/tRNA(Ser(UCN)) G7444A mutations. Their distinct sets of mtDNA polymorphism belonged to Eastern Asian haplogroup C4a1, while other previously identified six Chinese mitochondrial genomes harboring the C1494T mutation belong to haplogroups D5a2, D, R, and F1, respectively. This suggested that the C1494T or G7444A mutation occurred sporadically and multiplied through evolution of the mitochondrial DNA (mtDNA). The absence of functionally significant mutations in tRNA and rRNAs or secondary LHON mutations in their mtDNA suggest that these mtDNA haplogroup-specific variants may not play an important role in the phenotypic expression of the 12S rRNA C1494T and CO1/tRNA(Ser(UCN)) G7444A mutations in those Chinese families. However, aminoglycosides and other nuclear modifier genes play a modifying role in the phenotypic manifestation of the C1494T mutation in these Chinese families.     

基于12S rRNA基因的鹳形目系统发生关系

采用分子系统学的方法探讨鹳形目5个科之间的系统发生关系.文中测出鹳形目鸟类7种mtDNA 12SrRNA基因全序列,并结合来自Genbank的鹳形目另外7个物种及原鸡的同源区序列,经Clustal W软件对位排列后共1 009位点,包含405个变异位点,其中多态性位点381个,260个简约信息位点.基于上述序列数据,以原鸡为外群,使用距离邻接法、最大简约法、最大似然法及贝叶斯法分别重建了鹳形目5科14种的系统发生树.重建的系统发生树显示,内群中的14个种聚合为4支:鹮科构成第一支,聚在系统树的基部;锤头鹳科与鲸头鹳科聚为一支;鹭科和鹳科各自聚成一支.在比较不同建树方法的结果并进行合意树分析后认为:在鹳形目的系统发生中,鹮科可能是最早分化出的一支;锤头鹳科与鲸头鹳科之间的亲缘关系最近,它们祖先与鹭科、鹳科之间的分歧在时间上可能非常接近.鹳形目5个科之间的系统关系可以表示为:(鹮科,(鹭科,鹳科,(锤头鹳科,鲸头鹳科))).     

KpnI families of long, interspersed repetitive DNAs associated with the human β-globin gene cluster

KpnI families of long, interspersed repetitive DNAs are ubiquitous repetitive elements that occur in tens of thousands of copies in primate genomes. KpnI 1.2, 1.5 and two different KpnI 1.8-kb families were found within and flanking a 6.4-kb repeat beginning at 3 kb, 3' from the human β-globin gene. Thus, six different types of KpnI families have now been identified, and four of these are found next to each other in a specific 6.4-kb repeat. Clones of the distinct KpnI families were hybridized to clones of the 6.4-kb repeat and adjacent sequences encompassed within some 17.6 kb of DNA lying 3' to the β-globin gene cluster. The four KpnI families appear to make up the entire length of the 6.4-kb repeat. The linear order of the various cloned KpnI sequences in the repeat is 5'-pBK(1.8)26-pBK.(1.5)54-pBK(1.2)11-pBK(1.8)11-3'. KpnI 1.2-kb sequences were also detected downstream from the 6.4-kb repeat. As in the case of the KpnI 1.2 and 1.5-kb families, the two KpnI 1.8-kb sequence families described here each hybridized with about 15% of all plaques in two independently generated human genome libraries.     

Contributions to the Phylogeny of the Cyclophyllidea (Cestoda) Inferred from Mitochondrial 12S rDNA

A 314-bp fragment of the mitochondrial 12S rRNA gene from 21 cestodes species of eight families was synthesized by PCR with specially designed primers. These allowed amplification of parasite DNA without concomitant synthesis of host DNA. Phylogenetic trees were inferred from the sequence data using three methods (maximum parsimony, maximum likelihood, and Fitch–Margoliash). At the major nodes all three trees were similar. For the first time the genus Mesocestoides could be arranged into the Cyclophyllidea and a narrow relationship between the Mesocestoididae, Taeniidae, Hymenolepididae, Anoplocephalidae, and Dipylidiidae was shown. Members of the families Catenotaeniidae and a cluster of two families (Hymenolepididae and Dilepididae) form two monophyletic groups which derive prior to the remaining families of this phylogenetic study. A third and a fourth clear monophyletic group were formed by the Taeniidae and by the Mesocestoididae. A high degree of variation within the examined 304-bp fragment was observed between two isolates of Taenia taeniaeformis, supporting often discussed genetic heterogeneity within this species. In contrast, only one nucleotide exchange was found in 23 isolates of Echinococcus multilocularis of various geographic origin, indicating that this species is genetically homogenous. Received: 1 October 1997 / Accepted: 4 December 1997     

Characterization and functional identification of a novel plant 4,5-extradiol dioxygenase involved in betalain pigment biosynthesis in Portulaca grandiflora

Betalains are pigments that replace anthocyanins in the majority of families of the plant order Caryophyllales. Betalamic acid is the common chromophore of betalains. The key enzyme of the betalain biosynthetic pathway is an extradiol dioxygenase that opens the cyclic ring of dihydroxy-phenylalanine (DOPA) between carbons 4 and 5, thus producing an unstable seco-DOPA that rearranges nonenzymatically to betalamic acid. A gene for a 4,5-DOPA-dioxygenase has already been isolated from the fungus Amanita muscaria, but no homolog was ever found in plants. To identify the plant gene, we constructed subtractive libraries between different colored phenotypes of isogenic lines of Portulaca grandiflora (Portulacaceae) and between different stages of flower bud formation. Using in silico analysis of differentially expressed cDNAs, we identified a candidate showing strong homology at the level of translated protein with the LigB domain present in several bacterial extradiol 4,5-dioxygenases. The gene was expressed only in colored flower petals. The function of this gene in the betalain biosynthetic pathway was confirmed by biolistic genetic complementation in white petals of P. grandiflora genotypes lacking the gene for color formation. This gene named DODA is the first characterized member of a novel family of plant dioxygenases phylogenetically distinct from Amanita sp. DOPA-dioxygenase. Homologs of DODA are present not only in betalain-producing plants but also, albeit with some changes near the catalytic site, in other angiosperms and in the bryophyte Physcomitrella patens. These homologs are part of a novel conserved plant gene family probably involved in aromatic compound metabolism.     

DNA sequence,structure, and phylogenetic relationship of the small subunit rRNA coding region of mitochondrial DNA fromPodospora anserina

Summary DNA sequence analysis and the localization of the 5 and 3 termini by S1 mapping have shown that the mitochondrial (mt) small subunit rRNA coding region fromPodospora anserina is 1980 bp in length. The analogous coding region for mt rRNA is 1962 bp in maize, 1686 bp inSaccharomyces cerevisiae, and 956 bp in mammals, whereas its counterpart inEscherichia coli is 1542 bp. TheP. anserina mt 16S-like rRNA is 400 bases longer than that fromE. coli, but can be folded into a similar secondary structure. The additional bases appear to be clustered at specific locations, including extensions at the 5 and 3 termini. Comparison with secondary structure diagrams of 16S-like RNAs from several organisms allowed us to specify highly conserved and variable regions of this gene. Phylogenetic tree construction indicated that this gene is grouped with other mitochondrial genes, but most closely, as expected, with the fungal mitochondrial genes.     

Sequence studies on the soybean chloroplast 16S–23S rDNA spacer region

The sequence of the ribosomal spacer region of soybean chloroplast DNA including the 3 end of the 16S rRNA gene, the tRNA^Ala and tRNA^Ile genes (but not their introns), the three intergenic regions and the 5 end of the 23S rRNA gene, has been determined. This sequence has been compared to corresponding regions of other angiosperm chloroplast DNAs. Secondary structure models are proposed for the entirety of the intergenic regions a, b and c and for the flanking rRNA regions. A model for a common secondary structure of the ribosomal spacer intergenic regions from chloroplasts of higher plants is proposed, which is supported by comparative evidence.     

Phylogeny of Trichomonads Inferred from Small-Subunit rRNA Sequences

ABSTRACT. Small subunit (16S-like) ribosomal RNA sequences were obtained from representatives of all four families constituting the order Trichomonadida. Comparative sequence analysis revealed that the Trichomonadida are a monophyletic lineage and a deep branch of the eukaryotic tree. Relative to other early divergent eukaryotic assemblages the branching pattern within the Trichomonadida is very shallow. This pattern suggests the Trichomonadida radiated recently, perhaps in conjunction with their animal hosts. From a morphological perspective the Devescovinidae and Calonymphidae are considered more derived than the Monocercomonadidae and Trichomonadidae. Molecular trees inferred by distance, parsimony and likelihood techniques consistently show the Devescovinidae and Calonymphidae are the earliest diverging lineages within the Trichomonadida, however bootstrap values do not strongly support a particular branching order. In an analysis of all known 16S-like ribosomal RNA sequences, the Trichomonadida share most recent common ancestry with unidentified protists from the hindgut of the termite Reticulitermes flavipes. The position of two putative free-living trichomonads in the tree is indicative of derivation from symbionts rather than direct descent from some free-living ancestral trichomonad.     

A comparison of 18s ribosomal RNA and rubisco large subunit sequences for studying angiosperm phylogeny

Summary Partial sequences of 18s rRNA were obtained for 2 gymnosperms and 12 angiosperms from a wide range of families and these were analyzed with 5 other published sequences to form a phylogenetic tree. Using 16 published sequences of the large subunit of rubisco (rbcL), also from a wide range of angiosperm families, another phylogenetic tree was derived and the two approaches were compared. Both phylogenetic trees gave good grouping within families but in neither case was there resolution of the branching order of major taxa. Superficially the long rbcL sequences (whose base composition was homogeneous among all species) seemed very promising, but analysis showed that a large proportion of the variation did not affect the amino acid sequence. Although silent substitution contained some phylogenetic information, at the level required to order major taxa, much of it was random and obfuscating. It was concluded that neither macromolecule alone was likely to yield a solution to the problem of angiosperm phylogeny and therefore that studies of both, at least, will be required. For this reason, a method wa described for obtaining both DNA and RNA of good quality from the same preparation and which had been used successfully with a wide range of species including many with pungent leaves.     

Molecular phylogeny of a circum-global, diverse gastropod superfamily (Cerithioidea: Mollusca: Caenogastropoda): pushing the deepest phylogenetic limits of mitochondrial LSU rDNA sequences

The Cerithioidea is a very diverse group of gastropods with ca. 14 extant families and more than 200 genera occupying, and often dominating, marine, estuarine, and freshwater habitats. While the composition of Cerithioidea is now better understood due to recent anatomical and ultrastructural studies, the phylogenetic relationships among families remain chaotic. Morphology-based studies have provided conflicting views of relationships among families. We generated a phylogeny of cerithioideans based on mitochondrial large subunit rRNA and flanking tRNA gene sequences (total aligned data set 1873 bp). Nucleotide evidence and the presence of a unique pair of tRNA genes (i.e., threonine + glycine) between valine-mtLSU and the mtSSU rRNA gene support conclusions based on ultrastructural data that Vermetidae and Campanilidae are not Cerithioidea, certain anatomical similarities being due to convergent evolution. The molecular phylogeny shows support for the monophyly of the marine families Cerithiidae [corrected], Turritellidae, Batillariidae, Potamididae, and Scaliolidae as currently recognized. The phylogenetic data reveal that freshwater taxa evolved on three separate occasions; however, all three recognized freshwater families (Pleuroceridae, Melanopsidae, and Thiaridae) are polyphyletic. Mitochondrial rDNA sequences provide valuable data for testing the monophyly of cerithioidean [corrected] families and relationships within families, but fail to provide strong evidence for resolving relationships among families. It appears that the deepest phylogenetic limits for resolving caenogastropod relationships is less than about 245--241 mya, based on estimates of divergence derived from the fossil record.     

DNA sequence and secondary structures of the large subunit rRNA coding regions and its two class I introns of mitochondrial DNA fromPodospora anserina

Summary DNA sequence analysis has shown that the gene coding for the mitochondrial (mt) large subunit ribosomal RNA (rRNA) fromPodospora anserina is interrupted by two class I introns. The coding region for the large subunit rRNA itself is 3715 bp and the two introns are 1544 (r1) and 2404 (r2) bp in length. Secondary structure models for the large subunit rRNA were constructed and compared with the equivalent structure fromEscherichia coli 23S rRNA. The two structures were remarkably similar despite an 800-base difference in length. The additional bases in theP. anserina rRNA appear to be mostly in unstructured regions in the 3 part of the RNA. Secondary structure models for the two introns show striking similarities with each other as well as with the intron models from the equivalent introns inSaccharomyces cerevisiae, Neurospora crassa, andAspergillus nidulans. The long open reading frames in each intron are different from each other, however, and the nucleotide sequence similarity diverges as it proceeds away from the core structure. Each intron is located within regions of the large subunit rRNA gene that are highly conserved in both sequence and structure. Computer analysis showed that the open reading frame for intron r1 contained a common maturase-like polypeptide. The open reading frames of intron r2 apeared to be chimeric, displaying high sequence similarity with the open reading frames in the r1 and ATPase 6 introns ofN. crassa.     

新疆塔里木盆地可培养嗜盐放线菌系统发育多样性

应用纯培养手段和基于16S rRNA基因序列的系统发育分析,对从塔里木盆地高盐环境土壤样品中分离的18株可培养嗜盐放线菌多样性进行了研究.实验结果表明,18株嗜盐放线菌可3个(GlycomycetaceaePseudonocardineae和Nocardiopsaceae),在有效发表的5个属的嗜盐放线菌中有4个属的嗜盐放线菌被分离到.多数菌株属于Actinopolyspora属(38.9%),Nocardiopsis属(27.8%)和Streptomonospora属(22.2%),是塔里木盆地高盐环境中嗜盐放线菌的优势类群.这些分离菌株中,菌株YIM 92370与最近种的相似性为92%,在Glycomycetaceae科内形成一个独立的分支,极有可能代表Glycomycetaceae科的一个新属.研究结果表明塔里木盆地高盐环境中存在有较为丰富的嗜盐放线菌系统发育多样性,并且潜藏着新类型的放线菌资源.     

Nucleic acids in mummified plant seeds: screening of twelve specimens by gel-electrophoresis,molecular hybridization and DNA cloning

Summary Twelve seed specimens of varying ages and from different archaeological sites were analyzed for the presence of polymerized DNA and RNA. Amongst the samples tested, one of Vitis vinifera from an archaeological site in Iran (2,000–3,000 B.C.) was found to be completely devoid of nucleic acids. Zea mais seeds of Precolumbial age from Peru (about 800 A.D.) contained depolymerized DNA and RNA. Samples of Vitis vinifera and Rubus sp. from a Lombard archaeological site (800 A.D.) as well as radiocarbon dated seeds from the site of the Spring Sanctuary near Metaponto (I–IV century B.C.) were found to contain polymerized DNA and rRNA bands. However the electrophoretic properties of the rRNAs in one case and hybridization experiments performed with cloned seed DNA in the other, clearly demonstrated that the polymerized nucleic acids were not of plant origin.